aguirreg

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=====An anatomical template of human striate and extrastriate retinotopy=====

This page provides the templates described in this paper:

  *  NC Benson, OH Butt, DH Brainard, GK Aguirre (2014) Correction of distortion in flattened representations of the cortical surface allows prediction of V1-V3 functional organization from anatomy. //PLoS Comput. Biol//. **10**(3):e1003538. doi:10.1371/journal.pcbi.1003538

Please refer any questions to <aguirreg@mail.med.upenn.edu>.

This page describes a template of the human brain that can be used to predict with known accuracy and precision the retinotopic organization of early visual cortical areas V1, V2, and V3 based upon the sulcal topology of the cortical surface.

The template is comprised of cortical surface representations in [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat|MGH/MGZ format]] suitable for use in [[http://surfer.nmr.mgh.harvard.edu|FreeSurfer]]. This page provides links to download these files, access to the raw data used to construct the template, and additional information about the template not reported in the paper.

The template is free to use (with appropriate attribution) for academic or commercial purposes. The atlas may not be distributed for commercial gain.

For information on the use of the files available on this page for predicting the retinotopic organization of a subject, please see [[data_currbio_2012_benson#symmetric_hemisphere_template|our V1 page]], which describes the use of our previous V1 template, which is represented in the same format as our V1, V2, and V3 template.
=====Downloads=====

====File Formats====
The file formats used to distribute the template include:
  * **VTK Files**.  [[http://public.kitware.com/VTK/pdf/file-formats.pdf|Visualization Toolkit files]]
  * **MGH Files**.  The native file format used by FreeSurfer. All MGH files provided on this page are mapped to the [[data_currbio_2012_benson#symmetric_hemisphere_template|hemisphere-symmetric]] ''fsaverage_sym'' space.


====Templates====

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/angle-template.sym.mgh|angle-template.sym.mgh]]\\ \\ V1, V2, and V3 Polar Angle template - fsaverage_sym MGH overlay.</WRAP>

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/vtk_files/angle-template.sym.vtk|angle-template.sym.vtk]]\\ \\ V1, V2, and V3 Polar Angle template - fsaverage_sym VTK surface.</WRAP>\\

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/eccen-template.sym.mgh|eccen-template.sym.mgh]]\\ \\ V1, V2, and V3 Eccentricity template - fsaverage_sym MGH overlay.</WRAP>

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/vtk_files/eccen-template.sym.vtk|eccen-template.sym.vtk]]\\ \\ V1, V2, and V3 Eccentricity template - fsaverage_sym VTK surface.</WRAP>\\

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/mgh_files/areas-template.sym.mgh|areas-template.sym.mgh]]\\ \\ V1, V2, and V3 Area Definitions template - fsaverage_sym MGH overlay.</WRAP>

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/vtk_files/areas-template.sym.vtk|areas-template.sym.vtk]]\\ \\ V1, V2, and V3 Area Definitions template - fsaverage_sym VTK surface.</WRAP>


====Analysis and Simulation Code====

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/extrastriate-analysis.nb|extrastriate-analysis.nb]]\\ \\ Mathematica notebook containing all analysis and visualization code for this project - Mathematica notebook (.nb) format.</WRAP>

<WRAP LEFT download round box 33%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/extrastriate-analysis.pdf|extrastriate-analysis.pdf]]\\ \\ PDF rendering of the Mathematica analysis notebook containing all analysis and visualization code for this project.</WRAP>

<WRAP LEFT download round box 33%>**Repository**\\ \\ [[https://github.com/noahbenson/SpringRegister|gitHub]]\\ \\ C++ source code for the mass-spring-damper simulation engine used to register the functional data to the Schira model is freely available at the gitHub repository noahbenson/SpringRegister. </WRAP>

====Simulation Movie====

<WRAP LEFT download round box 76%>**Download**\\ \\ [[https://cfn.upenn.edu/aguirreg/public/ES_template/simulationData10.mov|simulationData10.mov]]\\ \\ Spring simulation movie (QuickTime). This movie shows the positions of the vertices, colored by aggregate measured polar angle, during the spring simulation used in this paper. The aggregate was produced using the 10° dataset.  Note that the level of confidence in each vertex is also shown by blending the polar angle color with the cortical surface color in the case of low-confidence measurements. \\ The movie shows every 50th frame of the simulation.</WRAP>
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